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Conformational changes of Adeno-associated Virus type 1 induced by genome packaging

by single particle (icosahedral) reconstruction, at 9.7 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 4.6, Made by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 4.6, Made by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 1838
AuthorsGerlach B, Kleinschmidt JA, Bottcher B
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 4.6, Made by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 4.6, Made by UCSF CHIMERA

Supplemental images

1838.png
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Diagram

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List of similar structure data about Omokage system
Article
Citation - Primary
ArticleJ. Mol. Biol., Vol. 409, Issue 3, Page 427-38, Year 2011
TitleConformational changes in adeno-associated virus type 1 induced by genome packaging.
AuthorsBritta Gerlach, Jürgen A Kleinschmidt, Bettina Böttcher
Division of Tumor Virology, German Cancer Research Center, Im Neuenheimerfeld, Heidelberg, Germany.
KeywordsCapsid (ultrastructure), Capsid Proteins (ultrastructure), Cryoelectron Microscopy (methods), Dependovirus (chemistry), Genome, Viral, Image Processing, Computer-Assisted (methods), Models, Molecular, Protein Conformation, Virus Assembly
LinksPII: S0022-2836(11)00351-2, DOI: 10.1016/j.jmb.2011.03.062, PubMed: 21463638
Map
FileEMD-1838.map ( map file in CCP4 format, 7445 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density

Histogram

Histogram (log scale)
Contour Level:4.6 (by author), 4.6 (movie #1):
Minimum - Maximum: -14.4597 - 24.9488
Average (Standard dev.): -0.00967426 (4.14727)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis Order : X Y Z
Dimensions : 123 123 123
Origin : 0 0 0
Limit : 122 122 122
Spacing : 123 123 123
Unit CellA = 123 A , B = 123 A , C = 123 A ,
alpha = 90 degrees , beta = 90 degrees , gamma = 90 degrees
Pixel Spacing
XYZ
EMDB info.111
CCP4 map header111
EM Navigator Movie #12.82.82.8
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z111
M x/y/z123123123
origin x/y/z0.0000.0000.000
length x/y/z123.000123.000123.000
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-30-24-70
NX/NY/NZ6149141
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS123123123
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-14.46024.949-0.010
Annotation DetailsMap of Adeno-associated virus Type 1, group 3 (partly-filled capsids).
Supplement
Images
Images

1838.png
Sample
NameAdeno-associated Virus Type 1
Number of Components1
Oligomeric StateVP1, VP2, and VP3 in T1 arrangement
DetailsRecombinant AAV1 capsid, particles belong to group 3 (partly filled).
Component #1: virus - AAV 1
Scientific nameAdeno-associated virus - 1
Common NameAAV 1
Scientific Name of SpeciesAdeno-associated virus - 1 (NCBI Taxonomy: 85106)
Common Name of SpeciesAAV 1
EmptyYes
EnvelopedNo
IsolateSEROTYPE
ClassVIRUS-LIKE PARTICLE
Natural SourceHost Species: Homo sapiens (NCBI Taxonomy: 9606)
Host Category: VERTEBRATES
ShellDiameter: 240 A
T Number: 1
Experiment
Sample Preparation
StainingVitrified.
Specimen Support Details400 mesh perforated carbon
Specimen Stateparticle
Vitrification
MethodBlot for 15 s before plunging
Cryogen NameETHANE
DetailsVitrification instrument: Controlled environment
Humidity100
InstrumentHOMEMADE PLUNGER
Temperature96 Kelvin
Imaging
MicroscopeFEI/PHILIPS CM200FEG
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage200 kV
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 50000 X,
AstigmatismAt 200,000 times magnification on graininess of carbon
Imaging ModeBRIGHT FIELD
Defocus1500 nm - 3500 nm
Specimen Holder
HolderEucentric ( GATAN LIQUID NITROGEN )
Temperature95 Kelvin
Camera
DetectorKodak SO163 film
Image Acquisition
ScannerZEISS SCAI
Number of Digital Images105
Sampling Size7 microns
Quant Bit Number8
DetailsData binning 2x2 pixels, before processing.
Processing
Methodsingle particle (icosahedral) reconstruction
3 D reconstruction
AlgorithmCross-common lines
SoftwareMRC
CTF CorrectionMaps during combination
Resolution By Author9.7
Resolution Method0.5
Single Particle
DetailsParticles were sorted according to their density profiles. This reconstruction represents group 3, which consists of partly filled capsids.
Number of Projections2430
Applied SymmetryI (icosahedral)
Download
Data from EMDB
Header (meta data in XML format)emd-1838.xml (7.3 KB)
Map dataemd_1838.map.gz (6.6 MB)
Images1838.png (615 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-1838
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.6 MB
.webm (WebM/VP8 format), 5.5 MB
Session file for UCSF-Chimera, 26.6 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.2 MB
.webm (WebM/VP8 format), 5.1 MB
Session file for UCSF-Chimera, 26.1 KB